Commit 9d7e1f8c authored by jayd1860's avatar jayd1860
Browse files

v1.18.4 

-- Convert SNIRF acquired data loading code from using high level to low level HDF5 functions to improve performance.
-- Fix some bugs in Logger class and in code that uses it. Change the way unit test code uses logger as well.
-- Other small performance improvements most notably in not using the slow str2cell() where it's not needed.
parent ba348dad

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_DatasetLoad.m

0 → 100644
+20 −0
Original line number Diff line number Diff line 
function val = HDF5_DatasetLoad(gid, name, val)



if nargin==2

    val = []; 

end



try

    dsetid = H5D.open(gid, name);

    val = H5D.read(dsetid);

    H5D.close(dsetid);    

catch ME

    switch(class(val))

        case 'char'

            val = '';

        case 'cell'

            val = {};

        otherwise            

            val = [];

    end

end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_GroupClose.m

0 → 100644
+6 −0
Original line number Diff line number Diff line 
function HDF5_GroupClose(fileobj, gid, fid)



H5G.close(gid);

if ischar(fileobj)

    H5F.close(fid);

end

DataTree/AcquiredData/DataFiles/Hdf5/HDF5_GroupOpen.m

0 → 100644
+15 −0
Original line number Diff line number Diff line 
function [gid, fid] = HDF5_GroupOpen(fileobj, location)



% Find data location

if ischar(fileobj)

    fid = H5F.open(fileobj);

else

    fid = fileobj;

end

try

    gid = H5G.open(fid, location);

catch

    gid = -1;

end

DataTree/AcquiredData/DataFiles/Hdf5/convertH5StrToStr.m

+5 −2
Original line number Diff line number Diff line
@@ -2,6 +2,9 @@ function snew = convertH5StrToStr(s) 


snew = '';

if iscell(s) || ischar(s)

    if size(s,1) > size(s,2)

        s = s';

    end

    snew = strtrim_improve(s);

elseif iswholenum(s)

    snew = char(s(:)');  % make sure it's row vector

DataTree/AcquiredData/DataFiles/Hdf5/h5load.m

+115 −49
Original line number Diff line number Diff line 
function varval = h5load(fname, varval, varname)

function data = h5load(filename, path)

%

% data = H5LOAD(filename)

% data = H5LOAD(filename, path_in_file)

%

% Load data in a HDF5 file to a Matlab structure.

%

% Parameters

% ----------

%

% filename

%     Name of the file to load data from

% path_in_file : optional

%     Path to the part of the HDF5 file to load

%



if nargin==1

    varname = '';

end

varval = h5loadvar(fname, varval, varname);

% Author: Pauli Virtanen <pav@iki.fi>

% This script is in the Public Domain. No warranty.



if nargin > 1

    path_parts = regexp(path, '/', 'split');

else

    path = '';

    path_parts = [];

end



loc = H5F.open(filename, 'H5F_ACC_RDONLY', 'H5P_DEFAULT');

try

    data = load_one(loc, path_parts, path);

    H5F.close(loc);

catch exc

    H5F.close(loc);

    rethrow(exc);

end



% ---------------------------------------------------------------------------

function varval = h5loadvar(fname, varval, varname)



% Simple matrices: uint, int, double, char, etc

if ~isstruct(varval) && ~isobject(varval)

% ---------------------------------------------------------------------

function data = load_one(loc, path_parts, full_path)

% Load a record recursively.



    % Create new leaf variable if it doesn't exist. 

    if exist(fname, 'file') && h5exist(h5info(fname), varname)

        varval = h5read(fname, varname);

    elseif exist(fname, 'file') && h5exist(h5info(fname), [varname, '_0'])

        switch(class(varval))

            case 'char'

                varval = '';

            case 'cell'

                varval = {};

            otherwise

                varval = [];                

        end

while ~isempty(path_parts) & strcmp(path_parts{1}, '')

    path_parts = path_parts(2:end);

end



% Structs and Classes

else

data = struct();



    props = propnames(varval(1));

    jj=1;

    while 1

num_objs = H5G.get_num_objs(loc);



        % Construct varname as it would appear in HDF5 file

        if isempty(varname) || varname(1)=='/'

            varname_jj = sprintf('%s_%d', varname, jj);

%

% Load groups and datasets

%

for j_item = 0:num_objs-1

    objtype = H5G.get_objtype_by_idx(loc, j_item);

    objname = H5G.get_objname_by_idx(loc, j_item);

    

    if objtype == 0

        % Group

        name = regexprep(objname, '.*/', '');

        

        if isempty(path_parts) | strcmp(path_parts{1}, name)

            if ~isempty(regexp(name,'^[a-zA-Z].*'))

                try

                    group_loc = H5G.open(loc, name);

                catch

                    d=1;

                end

                try

                    sub_data = load_one(group_loc, path_parts(2:end), full_path);

                    H5G.close(group_loc);

                catch exc

                    H5G.close(group_loc);

                    rethrow(exc);

                end

                if isempty(path_parts)

                    data = setfield(data, name, sub_data);

                else

            varname_jj = sprintf('/%s_%d', varname, jj);

                    data = sub_data;

                    return

                end

            end

        end

        

    elseif objtype == 1

        % Dataset

        name = regexprep(objname, '.*/', '');

        

        % Check if next struct or class element exists in HDF5 file

        if ~h5exist(h5info(fname), varname_jj);

            break;

        if isempty(path_parts) | strcmp(path_parts{1}, name)

            if ~isempty(regexp(name,'^[a-zA-Z].*'))

                dataset_loc = H5D.open(loc, name);

                try

                    sub_data = H5D.read(dataset_loc, 'H5ML_DEFAULT', 'H5S_ALL','H5S_ALL','H5P_DEFAULT');

                    H5D.close(dataset_loc);

                catch exc

                    H5D.close(dataset_loc);

                    rethrow(exc);

                end

                

        % Get values for all class/struct properties or fields

        for ii=1:length(props)

            subvarname = sprintf('%s/%s', varname_jj, props{ii});

            if jj>length(varval)

                if isstruct(varval)

                    varval(jj) = varval(1);

                sub_data = fix_data(sub_data);

                

                if isempty(path_parts)

                    data = setfield(data, name, sub_data);

                else

                    eval( sprintf('varval(jj) = %s();', class(varval(1))) );

                    data = sub_data;

                    return

                end

            end

        end

            varval_jj_prop = eval( sprintf('varval(jj).%s', props{ii}) );

            varval_jj_prop = h5loadvar(fname, varval_jj_prop, subvarname);

            eval( sprintf('varval(jj).%s = varval_jj_prop;', props{ii}) );

    end

        jj=jj+1;

end



% Check that we managed to load something if path walking is in progress

if ~isempty(path_parts)

    error(sprintf('Path "%s" not found in the HDF5 file', full_path));

end





% ---------------------------------------------------------------------

function data = fix_data(data)

% Fix some common types of data to more friendly form.



if isstruct(data)

    fields = fieldnames(data);

    if length(fields) == 2 & strcmp(fields{1}, 'r') & strcmp(fields{2}, 'i')

        if isnumeric(data.r) & isnumeric(data.i)

            data = data.r + 1j*data.i;

        end

    end

end



if isnumeric(data) & ndims(data) > 1

    % permute dimensions

    data = permute(data, fliplr(1:ndims(data)));

end

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